[Insight-developers] Re: Update on GE5 Image Reading (STILL NEED SCANS!)

[Bill Lorensen]

Steve,

It would be great if he could scan a phantom. There used to be a GE phantom
that was made of Plexiglas. I had scans of it in every direction, but I have
no idea where the data is.

Bill

On 10/24/07, Steve Pieper <pieper at bwh.harvard.edu> wrote:
>
> I talked with Marek today and in a couple weeks he'll have some scanner
> time and we'll try the following:
>
> - acquire various scan orientations (including oblique) of the same
> subject
> - acquire both structural and dwi
> - save as both dicom and ge native
>
> This will give us a nice data set for debugging these issues and the
> related (but even *more* complex!) issues with diffusion sequences.
>
> Thanks everybody for digging into this,
> -Steve
>
> p.s. Go Sox!
>
> Bill Lorensen wrote:
> > It was raining today and my golf buddy is in Florida for the winter...
> >
> > Retired Bill
> >
> >
> > On 10/24/07, *Hans Johnson* <hans-johnson at uiowa.edu
> > <mailto:hans-johnson at uiowa.edu>> wrote:
> >
> >     Bill,
> >
> >     THANKS.  Your efforts on this are greatly appreciated.  I'll try to
> >     test it out later this week.
> >
> >     Hans
> >     --
> >     Hans J. Johnson, Ph.D.
> >     Hans-johnson at uiowa.edu <mailto:Hans-johnson at uiowa.edu>
> >
> >     278 GH
> >     The University of Iowa
> >     Iowa City, IA 52241
> >     (319) 353 8587
> >
> >
> >
> ------------------------------------------------------------------------
> >     *From: *Bill Lorensen <bill.lorensen at gmail.com
> >     <mailto:bill.lorensen at gmail.com>>
> >     *Date: *Wed, 24 Oct 2007 17:38:29 -0400
> >     *To: *kent williams <norman-k-williams at uiowa.edu
> >     <mailto:norman-k-williams at uiowa.edu>>
> >     *Cc: *ITK < insight-developers at itk.org
> >     <mailto:insight-developers at itk.org>>, Hans Johnson
> >     <hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>>, Steve
> >     Pieper < pieper at bwh.harvard.edu <mailto:pieper at bwh.harvard.edu>>
> >     *Subject: *Re: Update on GE5 Image Reading (STILL NEED SCANS!)
> >
> >
> >     Kent,
> >
> >     My changes sort the files also, if necessary. Also, the origin
> >     computation was wrong.
> >
> >
> >     Bill
> >
> >     On 10/24/07, *kent williams* < norman-k-williams at uiowa.edu
> >     <mailto:norman-k-williams at uiowa.edu>> wrote:
> >
> >         Mea Maxima Culpa -- the GE file formats Image I/O stuff is the
> >         very first
> >         ITK code I wrote, and there is more than a little ugliness
> >         involved there
> >         unfortunately.  I was converting code from BRAINS2 to the ITK
> way.
> >
> >         Anyway, I have a fix that I can check in that makes images look
> >         much better.
> >         As near as I can figure, the sorting of slice files was
> >         backwards in some
> >         cases.  It was even worse than that really -- itk::GE5ImageIO
> >         was looking at
> >         fields in the GE5/Signa/Genesis file header that don't really
> >         mean what the
> >         code thought it meant.
> >
> >         Someone (Bill Lorensen is one suspect) added the code to
> >         generate direction
> >         cosines directly from the GE5 file header, so I started using
> >         that instead
> >         of undocumented fields in the header to recover the orientation.
> >          That
> >         DirCosine code is as far as I know correct.
> >
> >         But, the test images were coming in swapped in one dimension or
> >         another.
> >         What I finally figured out is that the code that sorted the 2D
> >         files before
> >         moving data into a 3D buffer wasn't using the right sort order,
> >         at all. So I
> >         added code to set the sort order right, based on the image
> >         orientation.
> >
> >         I THINK I have it licked but I'm still not finding good,
> >         unambiguous test
> >         data.  I can tell where the top of the skull and the nose are,
> >         but bilateral
> >         symmetry means I can't tell when there's a L/R swap.
> >
> >         Fucang was kind enough to find me a few good sample files.  But
> >         does anyone
> >         have any GE5 files where there's some indication of which is
> >         left and right?
> >         Something like the 'vitaman E cap on the left temple' trick
> >         would be ideal.
> >
> >         Speaking of sample files:
> >
> >         This directory
> >         http://128.196.98.224/Public/Imaging/Event/MGH/New/
> >         <http://128.196.98.224/Public/Imaging/Event/MGH/New/> is
> >         supposed to be an example of an axially oriented GE5 file.  If
> >         you load it
> >         into Slicer3 (for example) it looks way way ugly. Not clear to
> >         me why, but
> >         Slicer3 displays the volume as a skewed frustrum, as though
> >         every coronal
> >         slice is offset in the Y direction from it's neighbors.
> >
> >
> >
> >
>
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